chrX:154030648:C>T Detail (hg38) (MECP2)

Information

Genome

Assembly Position
hg19 chrX:153,296,099-153,296,099 View the variant detail on this assembly version.
hg38 chrX:154,030,648-154,030,648

HGVS

Type Transcript Protein
RefSeq NM_004992.3:c.1180G>A NP_004983.1:p.Glu394Lys
NM_001110792.1:c.1216G>A NP_001104262.1:p.Glu406Lys
NM_001316337.1:c.*552G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 300005 OMIM
HGNC 6990 HGNC
Ensembl ENSG00000169057 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv67029391 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2017-10-12 criteria provided, multiple submitters, no conflicts not specified germline maternal unknown Detail
Benign 2021-03-26 reviewed by expert panel Rett syndrome germline paternal unknown Detail
Benign 2024-01-31 criteria provided, single submitter Severe neonatal-onset encephalopathy with microcephaly germline Detail
Likely benign 2022-08-18 criteria provided, single submitter MECP2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.480 Mental Retardation, X-Linked, Syndromic 13 NA CLINVAR Detail
0.800 Rett syndrome NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001110792.2(MECP2):c.1216G>A (p.Glu406Lys) AND not specified ClinVar Detail
NM_001110792.2(MECP2):c.1216G>A (p.Glu406Lys) AND Rett syndrome ClinVar Detail
NM_001110792.2(MECP2):c.1216G>A (p.Glu406Lys) AND Severe neonatal-onset encephalopathy with microcep... ClinVar Detail
NM_001110792.2(MECP2):c.1216G>A (p.Glu406Lys) AND MECP2-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs63094662 dbSNP
Genome
hg38
Position
chrX:154,030,648-154,030,648
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.60to99.80
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs63094662
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0008
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12816
East Asian Chromosome Counts (ExAC)
6429
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
82722
Allele Counts in All Race (ExAC)
3
Heterozygous Counts in All Race (ExAC)
2
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.626604772611881E-5
East Asian Hemizygous Counts (ExAC)
0
Hemizygous Counts in All Race (ExAC)
1
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